Northern peatlands store globally significant carbon stocks and are major sources of dissolved organic carbon (DOC) to downstream waters, yet the hydrological mechanisms controlling water and waterborne carbon export remain poorly resolved. This uncertainty is particularly important in structurally complex landscapes where wetlandtype, peat thickness, and mineral substrate properties shift over short distances, potentially creating localized but highly connected flowpaths that are difficult to capture in landscape-scale models and monitoring frameworks. Here, hydrological conditions, geochemistry, and DOC concentrations were monitored over two growing seasons across a peatland–lake transition in Canada’s Precambrian Shield and integrated with subsurface flowpath modelling to determine how landscape structure and flowpath activation regulate water and DOC export.<br />Flowpath geometry remained stable despite substantial variation in water availability, indicating strong structural control by landscape morphology and subsurface properties. In contrast, water table dynamics varied among landscape units, constraining near-surface flowpath activation. Limited near-surface connectivity in upgradient wetlands was insufficient to explain persistent groundwater discharge at the outlet. Instead, evidence supports preferential subsurface flowpaths linking upgradient peatland units to a groundwater spring, sustaining discharge and episodically mobilizing DOC-rich waters. Catchment-scale annual DOC export to the downgradient lake was estimated between 3.1 and 14.1 g C m⁻² yr⁻¹. More than 20% of this DOC export originated from the single groundwater spring, demonstrating that small, preferentially connected areas can exert disproportionate control on peatland carbon loss to downstream aquatic ecosystems. These findings suggest that predicting aquatic carbon export from northern peatlands under climate change and land-use disturbance requires greater attention to subsurface structure, threshold-mediated connectivity, and localized flowpaths that may be overlooked when peatlands are treated as spatially uniform source areas.